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- PDB-1rt8: CRYSTAL STRUCTURE OF THE ACTIN-CROSSLINKING CORE OF SCHIZOSACCHAR... -

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Basic information

Entry
Database: PDB / ID: 1rt8
TitleCRYSTAL STRUCTURE OF THE ACTIN-CROSSLINKING CORE OF SCHIZOSACCHAROMYCES POMBE FIMBRIN
Componentsfimbrin
KeywordsSTRUCTURAL PROTEIN / Filamentous Actin Binding Domain (ABD) / Calponin Homology / Actin-Crosslinking
Function / homology
Function and homology information


actomyosin contractile ring organization / actin body / formin-nucleated actin cable organization / mitotic actomyosin contractile ring, distal actin filament layer / actin cortical patch organization / medial cortex / actin cortical patch localization / actin filament network formation / actin cortical patch / cell division site ...actomyosin contractile ring organization / actin body / formin-nucleated actin cable organization / mitotic actomyosin contractile ring, distal actin filament layer / actin cortical patch organization / medial cortex / actin cortical patch localization / actin filament network formation / actin cortical patch / cell division site / actin filament bundle / actin filament bundle assembly / actin filament / endocytosis / actin filament binding / calcium ion binding / cytoplasm
Similarity search - Function
Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2 Å
AuthorsKlein, M.G. / Shi, W. / Ramagopal, U. / Tseng, Y. / Wirtz, D. / Kovar, D.R. / Staiger, C.J. / Almo, S.C.
Citation
Journal: Structure / Year: 2004
Title: Structure of the actin crosslinking core of fimbrin.
Authors: Klein, M.G. / Shi, W. / Ramagopal, U. / Tseng, Y. / Wirtz, D. / Kovar, D.R. / Staiger, C.J. / Almo, S.C.
#1: Journal: Mol.Cell.Biol. / Year: 2001
Title: Interactions among a fibrin, a capping protein, and an actin-depolymerizing factor in organization of the fission yeast actin cytoskeleton
Authors: Nakano, K. / Satoh, K. / Morimatsu, A. / Ohnuma, M. / Mabuchi, I.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fimbrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9326
Polymers57,4511
Non-polymers4805
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.243, 84.243, 150.819
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein fimbrin


Mass: 57451.445 Da / Num. of mol.: 1 / Fragment: Actin-Crosslinking Core, amino acids 108-614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O59945
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 3300, MES, Lithium Sulfate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.9793
SYNCHROTRONAPS 19-BM20.9796
Detector
TypeIDDetectorDate
SBC-31CCDMar 12, 2003
SBC-32CCDMar 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97961
ReflectionResolution: 2→30 Å / Num. all: 42732 / Num. obs: 37818 / % possible obs: 95.2 % / Observed criterion σ(F): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 65

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXSphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: PDB ENTRY 1PXY

1pxy


Resolution: 2→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 3477 RANDOM
Rwork0.237 --
all-42732 -
obs-34533 -
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 25 104 3783

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